Deciphering the human genome, i.e., the sequencing of the entire genetic information of humans, was a milestone in molecular biological research. Research is now focused on deciphering the function of the genome and on the gene products, the proteins. Here one would like to have the most complete possible picture of all proteins expressed in a certain cell population or in a certain tissue. The identity and quantity of the proteins should be correlated to a certain development stage or to the physiological state of the cell or tissue. Thus one would like to obtain a picture of all proteins that is as accurate and quantitative as possible in order to come closer to a functional description. This research of the “post genome” era is also referred to as proteomics. Whereas the genome is basically a static entity, the proteome of a living organism is characterized by its ability to change depending on the temperature, nutrient milieu, and the action of stress or drugs. It therefore comprises the totality of the proteins that are synthesized by the genes of a cell or an organism under certain environmental conditions in various growth phases.
Proteomics is intended to yield new information on the function, regulation, and interaction of proteins by identifying and quantifying all proteins. In particular the aim is to reveal quantifiable differences between normal cells and “degenerate” cancer cells or differences in the protein repertoire of “diseased” and “healthy”. This in turn allows a specific search for therapeutically active substances.
In order to analyze a proteome, the total amount of proteins is separated into its individual components, i.e., the many thousands of individual proteins are physically separated from the mixture. This is usually achieved by so-called two-dimensional (2-D) electrophoresis. In this process, the total proteins from a cell population or tissue are isolated as quantitatively as possible. If necessary certain fractionation steps are also carried out if one wants to specifically examine only a certain fraction of the total proteins, e.g., proteins from certain cell organelles such as the mitochondria.
Then an isoelectric focusing (IEF) is carried out in the first dimension which separates the proteins in a special gel or on a solid support in a pH gradient on the basis of their isoelectric point (pI). The proteins migrate in the electrical field and are focused at their pI which is characteristic for each protein. This first step of isoelectric focusing requires certain electrophoresis equipment to hold membranes or strips with immobilized pH gradients or gels with ampholyte buffers. The isoelectric focusing process usually takes many hours (24 to 48 h).
After the isoelectric focusing is completed, the gels or membranes are usually removed from the first apparatus and equilibrated in an electrophoresis buffer containing SDS (sodium dodecyl sulfate). Then each gel or each membrane is placed on a new second gel in a second gel apparatus. These second gels consist of SDS/polyacrylamide. After applying an electrical potential perpendicular to the IEF gel, the focused proteins migrate into the second gel and are separated there according to their molecular weight. This electrophoretic separation can also take many hours (>16 h).
In the next step the proteins separated in this manner are visualized. This occurs by a staining step using Coomassie Brilliant Blue, colloidal Coomassie, silver nitrate, or fluorescent dyes (SYPRO Red, SYPRO Ruby). Subsequently the stained gel is photographed, usually with a digital imaging system, or the stained spots are documented. In order to be able to make a more accurate scientific statement, either all stained proteins or certain proteins of interest (e.g. those whose position and/or quantity has changed relative to a reference) are identified and characterized. This is normally carried out by mass spectroscopic methods. The most commonly used method is the analysis of peptide fragments of a certain spot by MALDI-TOF (matrix-assisted laser desorption/ionization time-of-flight) mass spectrometry. For this, a multistep processing of the individual stained protein spots is again carried out.
In the first step the stained protein spots are isolated from the gel in the smallest possible volume. This is carried out manually or with automatic software-controlled spot pickers. The small protein-containing pieces of gel (a few μl volume) are then incubated with a buffer which ensures that SDS and the dye are removed from the gel. Then the gel pieces are dried, taken up in a buffer suitable for protease digestion and incubated with a protease (usually trypsin). This cleaves the proteins in the gel into defined fragments. Subsequently the protein fragments (peptides) are washed out of the gel or eluted with ammonium bicarbonate.
The peptides isolated from the individual gel pieces are then applied separately to a support for mass spectrometry and subjected to mass spectrometry (MALDI-TOF) after drying and optionally recrystallization. The data from the mass spectrometry allow an unequivocal identification of the protein and a relative quantification of the amount of protein by comparison with suitable databases.
The classical 2-D electrophoresis method described above with processing for mass spectrometry has a number of disadvantages:                It requires relatively large amounts of total protein (milligram). These amounts are often not available especially for problems of particular interest e.g. when examining tumour tissue.        It is very time consuming and laborious.        It includes very many steps that in some cases can only be carried out manually.        It requires a large amount of equipment (IEF electrophoresis, SDS-PAGE electrophoresis, stainer, imager, spot-picker, gel piece incubator, dryer, automatic pipettor, etc.)        It only allows separation of proteins that are suitable for IEF. Many classes of protein and especially those that are of particular interest, e.g., membrane proteins/receptors, cell nuclei- or DNA-associated proteins, cannot be separated by IEF or not adequately.        The overall process is not very reproducible.        
Although electrophoresis chips have been described in the literature or in patent applications (U.S. Pat. No. 6,214,191, U.S. Pat. No. 5,599,432, EP 977030, WO 0058721; Becker et al., J. Micromech. Microeng. 1988, 8, 24) for two-dimensional separation of proteins, they are not yet available as a product or as prototypes and cannot be tested. Methods for optical detection were described for the further processing, but no data that were obtained by the method were shown. Although such chips have the advantage of being able to separate very small amounts of protein, it is, however, clear to a person skilled in the art that these very small amounts can hardly still be optically detected.